Speaking to Eurogamer, Julien Laferrière, associate producer of Assassin's Creed 3, said that AC3 could receive a sequel or two if the fans want them.
Julien said that Assassin's Creed 2 received so many sequels, because fans adored Ezio Auditore, and AC3 might have something similar in store for it if Connor is as beloved as Ezio. However, this isn't saying that anything is, or is not, in the works at this point; Julien had this to say:
"For Assassin's Creed 3 we got three years, and I think it shows. Assassin's Creed 3 is the product of three years of development, but [because of that] we also now have a new engine, AnvilNext. It's tough to answer that without compromising anything. I can't really answer that question because there's so many implications."
If Connor's story really does become as developed as Ezio's did, then the notion would raise a lot of questions. Granted, this is all speculation, so it's less than a grain of salt at this point, but how far would the story go into American history if AC3 had sequels?